SimBu

DOI: 10.18129/B9.bioc.SimBu    

This is the development version of SimBu; to use it, please install the devel version of Bioconductor.

Simulate Bulk RNA-seq Datasets from Single-Cell Datasets

Bioconductor version: Development (3.16)

SimBu can be used to simulate bulk RNA-seq datasets with known cell type fractions. You can either use your own single-cell study for the simulation or the sfaira database. Different pre-defined simulation scenarios exist, as are options to run custom simulations. Additionally, expression values can be adapted by adding an mRNA bias, which produces more biologically relevant simulations.

Author: Alexander Dietrich [aut, cre]

Maintainer: Alexander Dietrich <alex.dietrich at tum.de>

Citation (from within R, enter citation("SimBu")):

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SimBu")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SimBu")

 

HTML R Script Getting started
HTML R Script Inputs and Outputs
HTML R Script Introducing mRNA bias into simulations with scaling factors
HTML R Script Public Data Integration using Sfaira
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews RNASeq, SingleCell, Software
Version 0.99.14
In Bioconductor since BioC 3.16 (R-4.2)
License GPL-3 + file LICENSE
Depends
Imports basilisk, BiocParallel, data.table, dplyr, ggplot2, tools, Matrix (>= 1.3.3), methods, phyloseq, proxyC, RColorBrewer, RCurl, reticulate, sparseMatrixStats, SummarizedExperiment, tidyr
LinkingTo
Suggests curl, knitr, matrixStats, rmarkdown, Seurat, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL https://github.com/omnideconv/SimBu
BugReports https://github.com/omnideconv/SimBu/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SimBu_0.99.14.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/SimBu
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SimBu
Package Short Url https://bioconductor.org/packages/SimBu/
Package Downloads Report Download Stats

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